[ARVADOS] updated: 1.3.0-524-gc63b86e07
Git user
git at public.curoverse.com
Wed Mar 13 15:26:01 EDT 2019
Summary of changes:
sdk/cwl/arvados_cwl/fsaccess.py | 4 ++--
sdk/cwl/tests/test_submit.py | 10 +++++++---
2 files changed, 9 insertions(+), 5 deletions(-)
via c63b86e079325b1d6b5a5ae3d9b06c231fad4bae (commit)
from 5450736979761397688dd6cf84a0df2ed01133cf (commit)
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commit c63b86e079325b1d6b5a5ae3d9b06c231fad4bae
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Wed Mar 13 15:25:33 2019 -0400
14322: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index d5866e728..6eb1bf640 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -265,8 +265,8 @@ class CollectionFetcher(DefaultFetcher):
locator = baseparts.pop(0)
if (basesp.scheme == "keep" and
- (not arvados.util.keep_locator_pattern.match(pdh)) and
- (not arvados.util.collection_uuid_pattern.match(pdh))):
+ (not arvados.util.keep_locator_pattern.match(locator)) and
+ (not arvados.util.collection_uuid_pattern.match(locator))):
raise IOError(errno.EINVAL, "Invalid Keep locator", base_url)
if urlsp.path.startswith("/"):
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 76b0f89f1..4e4ab7277 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1430,8 +1430,10 @@ class TestSubmit(unittest.TestCase):
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
+ @mock.patch("arvados.collection.CollectionReader")
@stubs
- def test_submit_uuid_inputs(self, stubs):
+ def test_submit_uuid_inputs(self, stubs, collectionReader):
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
def list_side_effect(**kwargs):
m = mock.MagicMock()
if "count" in kwargs:
@@ -1452,7 +1454,6 @@ class TestSubmit(unittest.TestCase):
expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
- del expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['size']
stubs.api.collections().list.assert_has_calls([
mock.call(count='none',
@@ -1496,8 +1497,11 @@ class TestSubmit(unittest.TestCase):
finally:
cwltool_logger.removeHandler(stderr_logger)
+ @mock.patch("arvados.collection.CollectionReader")
@stubs
- def test_submit_unknown_uuid_inputs(self, stubs):
+ def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
+
capture_stderr = io.StringIO()
cwltool_logger = logging.getLogger('cwltool')
stderr_logger = logging.StreamHandler(capture_stderr)
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